1a. Objectives (from AD-416)
1) Use the BovineSNP50 assay to provide high-accuracy predictions of genetic merit to U.S. dairy and beef breeds. 2) Enable the adoption of WGEAS by developing low-density and low-cost SNP assays for: a) intermediate-accuracy genetic prediction, b) mate selection, and c) parentage verification and traceability. 3) Develop, adapt and optimize statistical metodologies to: a) fully integrate SNP genotype or haplotype effects into existing genetic evaluation technologies, and b) supplement or replace pedigree data. 4)Collaborate and coordinate U.S. and European Union WGEAS activities.
1b. Approach (from AD-416)
1. Collect genotypic data using the bovineSNP50 in both dairy and beef cattle breeding programs. 2. Develop statistical algorithms needed to implement whole genome enabled animal selection specific to dairy and beef cattle populations as needed. 3. Determine subset of markers needed for low density SNP assay for application to parentage verification and reduced accuracy genetic prediction. 4. Collaborate with many organizations to utilize data generated by this project as well as other projects to obtain maximum utilization of resources generated.
3. Progress Report
The first objective to provide high-accuracy predictions of genetic merit enhanced by DNA marker data (BovineSNP50) in U.S. cattle has been met in dairy cattle and progress has been achieved in beef cattle. Genetic evaluations using genomic data have been considered “official” evaluations for Holstein and Jersey since January 2009 and Brown Swiss since August, 2009. For Angus cattle, a targeted 384 SNP panel was developed and commercialized with the most predictive SNP for Heifer Pregnancy Rate, Ribeye Muscle Area, Marbling, and Yearling Weight. The next objective was to enable the adoption of whole genome enabled animal selection (WGEAS) by developing low-density and low-cost SNP assays for: a) intermediate-accuracy genetic prediction, b) mate selection, and c) parentage verification and traceability. Development of a 96-SNP set for parentage has been completed. This set of SNP has been identified as a candidate list to replace the current list of microsatellites by the International Society of Animal Genetics. Additionally, this list has been deployed in at least 1 commercial assay and is under consideration by several other vendors. The third objective, to conduct SNP discovery and contribute to the development of an ultrahigh-density SNP assay was completed. An international consortium produced whole genome sequence data on nearly 300 individual animals including a 60X coverage of the genomes of 6 important breeds of cattle conducted as part of this project. Bioinformatic analysis of these data identified more than 45 million high-quality SNP that were identified as being variable in at least 2 different cattle breeds. As part of the collaboration, an assay was designed using these SNP, and Illumina has marketed an 800K assay. This density of SNP is expected to allow the development of across-breed genetic predictions from the analysis of genotypes produced on animals from multiple breeds, where smaller breed numbers have impeded implementation of WGEAS due to accuracies for genetic prediction being well below those achieved by >10,000 Holsteins. The fourth objective is to develop, adapt and optimize statistical methodologies to: a) fully integrate SNP genotype or haplotype effects into existing genetic evaluation technologies, and b) supplement or replace pedigree data, is progressing. The final objective, to collaborate and coordinate U.S. and European Union WGEAS activities began this year. A large meeting of researchers contributing to this project as well as several European projects met at the Plant and Animal Genome conference to better foster collaboration and reduce duplication. Monitoring activities associated with this project included regular email correspondence and regular conference calls. This research supports two objectives of its related in-house project: 1) to use genotypic data and resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole genome selection and enhanced parentage verification approaches (obj. #2) and 2) to characterize conserved genome elements and identify functional genetic variation (obj. #3).